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Find video protocols related to scientific articles indexed in Pubmed.
Metabolomics in asthma.
Adv. Exp. Med. Biol.
PUBLISHED: 05-30-2014
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Asthma and airway inflammation are responses to infectious stimuli and the mechanisms of how they are mediated, whether by the innate or adaptive immune response systems, are complex and results in a broad spectrum of possible metabolic products. In principle, a syndrome such as asthma should have a characteristic temporal-spatial metabolic signature indicative of its current state and the constituents that caused it. Generally, the term metabolomics refers to the quantitative analysis of sets of small compounds from biological samples with molecular masses less than 1 kDa so unambiguous identification can be difficult and usually requires sophisticated instrumentation. The practical success of clinical metabolomics will largely hinge on a few key issues such as the ability to capture a readily available biofluid that can be analyzed to identify metabolite biomarkers with the required sensitivity and specificity in a cost-effective manner in a clinical setting. In this chapter, we review the current state of the metabolomics of asthma and airway inflammation with a focus on the different methods and instrumentation being used for the discovery of biomarkers in research and their future translation into the clinic as diagnostic aids for the choice of patient-specific therapies.
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Cognitive enhancing treatment with a PPAR? agonist normalizes dentate granule cell presynaptic function in Tg2576 APP mice.
J. Neurosci.
PUBLISHED: 01-17-2014
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Hippocampal network hyperexcitability is considered an early indicator of Alzheimer's disease (AD) memory impairment. Some AD mouse models exhibit similar network phenotypes. In this study we focused on dentate gyrus (DG) granule cell spontaneous and evoked properties in 9-month-old Tg2576 mice that model AD amyloidosis and cognitive deficits. Using whole-cell patch-clamp recordings, we found that Tg2576 DG granule cells exhibited spontaneous EPSCs that were higher in frequency but not amplitude compared with wild-type mice, suggesting hyperactivity of DG granule cells via a presynaptic mechanism. Further support of a presynaptic mechanism was revealed by increased I-O relationships and probability of release in Tg2576 DG granule cells. Since we and others have shown that activation of the peroxisome proliferator-activated receptor gamma (PPAR?) axis improves hippocampal cognition in mouse models for AD as well as benefitting memory performance in some humans with early AD, we investigated how PPAR? agonism affected synaptic activity in Tg2576 DG. We found that PPAR? agonism normalized the I-O relationship of evoked EPSCs, frequency of spontaneous EPSCs, and probability of release that, in turn, correlated with selective expression of DG proteins essential for presynaptic SNARE function that are altered in patients with AD. These findings provide evidence that DG principal cells may contribute to early AD hippocampal network hyperexcitability via a presynaptic mechanism, and that hippocampal cognitive enhancement via PPAR? activation occurs through regulation of presynaptic vesicular proteins critical for proper glutamatergic neurotransmitter release, synaptic transmission, and short-term plasticity.
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Caspase-1/ASC Inflammasome-Mediated Activation of IL-1?-ROS-NF-?B Pathway for Control of Trypanosoma cruzi Replication and Survival Is Dispensable in NLRP3-/- Macrophages.
PLoS ONE
PUBLISHED: 01-01-2014
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In this study, we have utilized wild-type (WT), ASC-/-, and NLRP3-/- macrophages and inhibition approaches to investigate the mechanisms of inflammasome activation and their role in Trypanosoma cruzi infection. We also probed human macrophages and analyzed published microarray datasets from human fibroblasts, and endothelial and smooth muscle cells for T. cruzi-induced changes in the expression genes included in the RT Profiler Human Inflammasome arrays. T. cruzi infection elicited a subdued and delayed activation of inflammasome-related gene expression and IL-1? production in m?s in comparison to LPS-treated controls. When WT and ASC-/- macrophages were treated with inhibitors of caspase-1, IL-1?, or NADPH oxidase, we found that IL-1? production by caspase-1/ASC inflammasome required reactive oxygen species (ROS) as a secondary signal. Moreover, IL-1? regulated NF-?B signaling of inflammatory cytokine gene expression and, subsequently, intracellular parasite replication in macrophages. NLRP3-/- macrophages, despite an inability to elicit IL-1? activation and inflammatory cytokine gene expression, exhibited a 4-fold decline in intracellular parasites in comparison to that noted in matched WT controls. NLRP3-/- macrophages were not refractory to T. cruzi, and instead exhibited a very high basal level of ROS (>100-fold higher than WT controls) that was maintained after infection in an IL-1?-independent manner and contributed to efficient parasite killing. We conclude that caspase-1/ASC inflammasomes play a significant role in the activation of IL-1?/ROS and NF-?B signaling of cytokine gene expression for T. cruzi control in human and mouse macrophages. However, NLRP3-mediated IL-1?/NF?B activation is dispensable and compensated for by ROS-mediated control of T. cruzi replication and survival in macrophages.
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Environmental enrichment alters protein expression as well as the proteomic response to cocaine in rat nucleus accumbens.
Front Behav Neurosci
PUBLISHED: 01-01-2014
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Prior research demonstrated that environmental enrichment creates individual differences in behavior leading to a protective addiction phenotype in rats. Understanding the mechanisms underlying this phenotype will guide selection of targets for much-needed novel pharmacotherapeutics. The current study investigates differences in proteome expression in the nucleus accumbens of enriched and isolated rats and the proteomic response to cocaine self-administration using a liquid chromatography mass spectrometry (LCMS) technique to quantify 1917 proteins. Results of complementary Ingenuity Pathways Analyses (IPA) and gene set enrichment analyses (GSEA), both performed using protein quantitative data, demonstrate that cocaine increases vesicular transporters for dopamine and glutamate as well as increasing proteins in the RhoA pathway. Further, cocaine regulates proteins related to ERK, CREB and AKT signaling. Environmental enrichment altered expression of a large number of proteins implicated in a diverse number of neuronal functions (e.g., energy production, mRNA splicing, and ubiquitination), molecular cascades (e.g., protein kinases), psychiatric disorders (e.g., mood disorders), and neurodegenerative diseases (e.g., Huntington's and Alzheimer's diseases). Upregulation of energy metabolism components in EC rats was verified using RNA sequencing. Most of the biological functions and pathways listed above were also identified in the Cocaine X Enrichment interaction analysis, providing clear evidence that enriched and isolated rats respond quite differently to cocaine exposure. The overall impression of the current results is that enriched saline-administering rats have a unique proteomic complement compared to enriched cocaine-administering rats as well as saline and cocaine-taking isolated rats. These results identify possible mechanisms of the protective phenotype and provide fertile soil for developing novel pharmacotherapeutics. Proteomics data are available via ProteomeXchange with identifier PXD000990.
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Vaccines based on structure-based design provide protection against infectious diseases.
Expert Rev Vaccines
PUBLISHED: 10-04-2013
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Vaccines elicit immune responses, provide protection against microorganisms and are considered as one of the most successful medical interventions against infectious diseases. Vaccines can be produced using attenuated virus or bacteria, recombinant proteins, bacterial polysaccharides, carbohydrates or plasmid DNA. Conventional vaccines rely on the induction of immune responses against antigenic proteins to be effective. The genetic diversity of microorganisms, coupled with the high degree of sequence variability in antigenic proteins, presents a challenge to developing broadly effective conventional vaccines. The observation that whole protein antigens are not necessarily essential for inducing immunity has led to the emergence of a new branch of vaccine design termed structural vaccinology. Structure-based vaccines are designed on the rationale that protective epitopes should be sufficient to induce immune responses and provide protection against pathogens. Recent studies demonstrated that designing structure-based vaccine candidates with multiple epitopes induce a higher immune response. As yet there are no commercial vaccines available based on structure-based design and most of the structure-based vaccine candidates are in the preclinical stages of development. This review focuses on recent advances in structure-based vaccine candidates and their application in providing protection against infectious diseases.
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Structure-based vaccines provide protection in a mouse model of ehrlichiosis.
PLoS ONE
PUBLISHED: 08-18-2011
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Recent advances in bioinformatics have made it possible to predict the B cell and T cell epitopes of antigenic proteins. This has led to design of peptide based vaccines that are more specific, safe, and easy to produce. The obligately intracellular gram negative bacteria Ehrlichia cause ehrlichioses in humans and animals. As yet there are no vaccines to protect against Ehrlichia infection.
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Effects of progesterone treatment on expression of genes involved in uterine quiescence.
Reprod Sci
PUBLISHED: 07-29-2011
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An important action of progesterone during pregnancy is to maintain the uterus in a quiescent state and thereby prevent preterm labor. The causes of preterm labor are not well understood, so progesterone action on the myometrium can provide clues about the processes that keep the uterus from contracting prematurely. Accordingly, we have carried out Affymetrix GeneChip analysis of progesterone effects on gene expression in immortalized human myometrial cells cultured from a patient near the end of pregnancy. Progesterone appears to inhibit uterine excitability by a number of mechanisms, including increased expression of calcium and voltage-operated K(+) channels, which dampens the electrical activity of the myometrial cell, downregulation of agents, and receptors involved in myometrial contraction, reduction in cell signal components that lead to increased intracellular Ca(2+) concentrations in response to contractile stimuli, and downregulation of proteins involved in the cross-linking of actin and myosin filaments to produce uterine contractions.
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Bone disorders in chronic liver diseases.
Curr Gastroenterol Rep
PUBLISHED: 04-22-2011
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Bone disease is a major complication of chronic liver disease. Osteomalacia is quite uncommon despite low vitamin D levels in the majority of patients with cirrhosis. In contrast, osteoporosis is quite common, occurring in up to 50% of patients. Osteoporosis can result in spontaneous or low-impact fractures in patients with chronic liver diseases, adversely affecting morbidity, quality of life, and survival. The general biology of osteoporosis, including its pathogenesis, diagnostic tools, and rationale for treatment, have been determined largely empirically from studies of postmenopausal women with osteoporosis. Treatment regimens with modification of risk factors, use of vitamin D, and supplementation with calcium and bisphosphonates have been shown to be effective in select groups of patients with chronic liver diseases.
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Biliverdin inhibits hepatitis C virus nonstructural 3/4A protease activity: mechanism for the antiviral effects of heme oxygenase?
Hepatology
PUBLISHED: 11-25-2010
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Induction of heme oxygenase-1 (HO-1) inhibits hepatitis C virus (HCV) replication. Of the products of the reaction catalyzed by HO-1, iron has been shown to inhibit HCV ribonucleic acid (RNA) polymerase, but little is known about the antiviral activity of biliverdin (BV). Herein, we report that BV inhibits viral replication and viral protein expression in a dose-dependent manner in replicons and cells harboring the infectious J6/JFH construct. Using the SensoLyte 620 HCV Protease Assay with a wide wavelength excitation/emission (591 nm/622 nm) fluorescence energy transfer peptide, we found that both recombinant and endogenous nonstructural 3/4A (NS3/4A) protease from replicon microsomes are potently inhibited by BV. Of the tetrapyrroles tested, BV was the strongest inhibitor of NS3/4A activity, with a median inhibitory concentration (IC(50)) of 9 ?M, similar to that of the commercial inhibitor, AnaSpec (Fremont, CA) #25346 (IC(50) 5 ?M). Lineweaver-Burk plots indicated mixed competitive and noncompetitive inhibition of the protease by BV. In contrast, the effects of bilirubin (BR) on HCV replication and NS3/4A were much less potent. Because BV is rapidly converted to BR by biliverdin reductase (BVR) intracellularly, the effect of BVR knockdown on BV antiviral activity was assessed. After greater than 80% silencing of BVR, inhibition of viral replication by BV was enhanced. BV also increased the antiviral activity of ?-interferon in replicons. Conclusion: BV is a potent inhibitor of HCV NS3/4A protease, which likely contributes to the antiviral activity of HO-1. These findings suggest that BV or its derivatives may be useful in future drug therapies targeting the NS3/4A protease.
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Requirement of TGFbeta signaling for SMO-mediated carcinogenesis.
J. Biol. Chem.
PUBLISHED: 09-21-2010
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Hedgehog (Hh) signaling, via the key signal transducer Smoothened (SMO) and Gli transcription factors, is essential for embryonic development and carcinogenesis. At present, the molecular mechanism of Hh signaling-mediated carcinogenesis is not completely understood. Using a mouse model (K14cre/R26SmoM2) of SMO-mediated basal cell carcinoma development, we identified TGF?2 as a major Hh-regulated gene. TGF?2 expression was high in the keratinocytes, with activated TGF? signaling (indicated by elevated expression of phosphorylated SMAD2/3) detected in both tumor and stroma. The significance of TGF? signaling for SMO function was demonstrated in two assays. Down-regulation of TGF?2 expression prevented Hh signaling-dependent osteoblast differentiation and motor neuron differentiation. Furthermore, inhibition of TGF? signaling by TGF? receptor I inhibitor SD208 significantly reduced tumor area in K14cre/R26SmoM2 mice. Tumor shrinkage in mice was associated with an increased number of lymphocytes, suggesting an immune suppression role of TGF? signaling. The relevance of our results to human cancer is reflected by the fact that human basal cell carcinomas, which almost always harbor activated Hh signaling, have activated TGF? signaling, as indicated by high levels of phosphorylated SMAD2 and SMAD3 in tumor and stroma. Together, our data indicate that TGF? signaling is critical for Hh signaling-mediated carcinogenesis.
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¹H and ³¹P NMR lipidome of ethanol-induced fatty liver.
Alcohol. Clin. Exp. Res.
PUBLISHED: 08-05-2010
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?Hepatic steatosis (fatty liver), an early and reversible stage of alcoholic liver disease, is characterized by triglyceride deposition in hepatocytes, which can advance to steatohepatitis, fibrosis, cirrhosis, and ultimately to hepatocellular carcinoma. In the present work, we studied altered plasma and hepatic lipid metabolome (lipidome) to understand the mechanisms and lipid pattern of early-stage alcohol-induced-fatty liver.
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Training for a career in hepatology: which path to take?
Curr Gastroenterol Rep
PUBLISHED: 04-29-2010
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Hepatology has matured significantly over the past two decades, and most gastroenterologists now believe that it is a distinct subspecialty. An unmet public health need exists for professional expertise in the care of patients with liver diseases. However, our current training programs are struggling to adequately recruit and train physicians with the appropriate expertise in advanced and transplant hepatology. This review briefly summarizes the recent discoveries and developments in clinical hepatology, describes the past and current training paradigms, and suggests potential pathways to improve the number and quality of physicians trained in advanced and transplant hepatology.
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1H NMR-based metabonomic investigation of tributyl phosphate exposure in rats.
Toxicol. Lett.
PUBLISHED: 04-18-2010
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Tributyl phosphate (TBP) is a toxic organophosphorous compound widely used in many industrial applications, including significant usage in nuclear processing. The industrial application of this chemical is responsible for occupational exposure and environmental pollution. In this study, (1)H NMR-based metabonomics has been applied to investigate the metabolic response to TBP exposure. Male Sprague-Dawley rats were given a TBP-dose of 15 mg/kg body weight, followed by 24h urine collection, as was previously demonstrated for finding most of the intermediates of TBP. High-resolution (1)H NMR spectroscopy of urine samples in conjunction with statistical pattern recognition and compound identification allowed for the metabolic changes associated with TBP treatment to be identified. Discerning NMR spectral regions corresponding to three TBP metabolites, dibutyl phosphate (DBP), N-acetyl-(S-3-hydroxybutyl)-L-cysteine and N-acetyl-(S-3-oxobutyl)-L-cysteine, were identified in TBP-treated rats. In addition, the (1)H NMR spectra revealed TBP-induced variations of endogenous urinary metabolites including benzoate, urea, and trigonelline along with metabolites involved in the Krebs cycle including citrate, cis-aconitate, trans-aconitate, 2-oxoglutarate, succinate, and fumarate. These findings indicate that TBP induces a disturbance to the Krebs cycle energy metabolism and provides a biomarker signature of TBP exposure. We show that three metabolites of TBP, dibutylphosphate, N-acetyl-(S-3-hydroxybutyl)-L-cysteine and N-acetyl-(S-3-oxobutyl)-L-cysteine, which are not present in the control groups, are the most important factors in separating the TBP and control groups (p<0.0023), while the endogenous compounds 2-oxoglutarate, benzoate, fumarate, trigonelline, and cis-aconetate were also important (p<0.01).
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The "iowa get screened" colon cancer screening program.
J Prim Care Community Health
PUBLISHED: 04-01-2010
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To implement a colon cancer screening program for uninsured or underinsured Iowans.
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Proteomic analysis of Pichindé virus infection identifies differential expression of prothymosin-alpha.
J. Biomed. Biotechnol.
PUBLISHED: 03-04-2010
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The arenaviruses include a number of important pathogens including Lassa virus and Junin virus. Presently, the only treatment is supportive care and the antiviral Ribavirin. In the event of an epidemic, patient triage may be required to more effectively manage resources; the development of prognostic biomarker signatures, correlating with disease severity, would allow rational triage. Using a pair of arenaviruses, which cause mild or severe disease, we analyzed extracts from infected cells using SELDI mass spectrometry to characterize potential biomarker profiles. EDGE analysis was used to analyze longitudinal expression differences. Extracts from infected guinea pigs revealed protein peaks which could discriminate between mild or severe infection, and between times post-infection. Tandem mass-spectrometry identified several peaks, including the transcriptional regulator prothymosin-alpha. Further investigation revealed differences in secretion of this peptide. These data show proof of concept that proteomic profiling of host markers could be used as prognostic markers of infectious disease.
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Altered retinoic acid metabolism in diabetic mouse kidney identified by O isotopic labeling and 2D mass spectrometry.
PLoS ONE
PUBLISHED: 02-02-2010
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Numerous metabolic pathways have been implicated in diabetes-induced renal injury, yet few studies have utilized unbiased systems biology approaches for mapping the interconnectivity of diabetes-dysregulated proteins that are involved. We utilized a global, quantitative, differential proteomic approach to identify a novel retinoic acid hub in renal cortical protein networks dysregulated by type 2 diabetes.
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Pathway signature and cellular differentiation in clear cell renal cell carcinoma.
PLoS ONE
PUBLISHED: 01-28-2010
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Clear cell renal cell carcinoma (ccRCC) is the most common kidney cancer. The purpose of this study is to define a biological pathway signature and a cellular differentiation program in ccRCC.
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Attenuated and lethal variants of Pichindé virus induce differential patterns of NF-kappaB activation suggesting a potential target for novel therapeutics.
Viral Immunol.
PUBLISHED: 12-03-2009
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Lassa virus pathogenesis is believed to involve dysregulation of cytokines. We have previously shown nuclear factor-kappaB (NF-kappaB) inhibition using a BSL-2 model for Lassa fever. Here we further define the potential mechanism for NF-kappaB inhibition as involving increased levels of repressive p50/p50 homodimers, and suggest a novel therapeutic strategy that acts via modulation of host signaling.
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Allergen challenge induces Ifng dependent GTPases in the lungs as part of a Th1 transcriptome response in a murine model of allergic asthma.
PLoS ONE
PUBLISHED: 07-30-2009
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According to the current paradigm, allergic airway inflammation is mediated by Th2 cytokines and pro-inflammatory chemokines. Since allergic inflammation is self-limited, we hypothesized that allergen challenge simultaneously induces anti-inflammatory genes to counter-balance the effects of Th2 cytokines and chemokines. To identify these putative anti-inflammatory genes, we compared the gene expression profile in the lungs of ragweed-sensitized mice four hours after challenge with either PBS or ragweed extract (RWE) using a micro-array platform. Consistent with our hypothesis, RWE challenge concurrently upregulated Th1-associated early target genes of the Il12/Stat4 pathway, such as p47 and p65 GTPases (Iigp, Tgtp and Gbp1), Socs1, Cxcl9, Cxcl10 and Gadd45g with the Th2 genes Il4, Il5, Ccl2 and Ccl7. These Th1-associated genes remain upregulated longer than the Th2 genes. Augmentation of the local Th1 milieu by administration of Il12 or CpG prior to RWE challenge further upregulated these Th1 genes. Abolition of the Th1 response by disrupting the Ifng gene increased allergic airway inflammation and abrogated RWE challenge-induced upregulation of GTPases, Cxcl9, Cxcl10 and Socs1, but not Gadd45g. Our data demonstrate that allergen challenge induces two sets of Th1-associated genes in the lungs: 1) Ifng-dependent genes such as p47 and p65 GTPases, Socs1, Cxcl9 and Cxcl10 and 2) Ifng-independent Th1-inducing genes like Gadd45g. We propose that allergen-induced airway inflammation is regulated by simultaneous upregulation of Th1 and Th2 genes, and that persistent unopposed upregulation of Th1 genes resolves allergic inflammation.
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Investigation of chemometric instrumental transfer methods for high-resolution NMR.
Anal. Chem.
PUBLISHED: 05-30-2009
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The implementation of direct standardization (DS), piecewise direct standardization (PDS), and double-window piecewise direct standardization (DWPDS) instrumental transfer techniques for high-resolution (1)H NMR spectral data was explored. The ability to transfer a multivariate calibration model developed for a "master or target" NMR instrument configuration to seven different ("secondary") NMR instrument configurations was measured. Partial least-squares (PLS) calibration of glucose, glycine, and citrate metabolite relative concentrations in model mixtures following mapping of the secondary instrumental configurations using DS, PDS, or DWPDS instrumental transfer allowed the performance of the different transfer methods to be assessed. Results from these studies suggest that DS and PDS transfer techniques produce similar improvements in the error of prediction compared to each other and provide a significant improvement over standard spectral preprocessing techniques including reference deconvolution and spectral binning. The DS instrumental transfer method produced the largest percent improvement in the predictions of concentrations for these model mixtures but, in general, required that additional transfer calibration standards be used. Limitations of the different instrumental transfer methods with respect to sample subset selection are also discussed.
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Integrin alpha6beta4 controls the expression of genes associated with cell motility, invasion, and metastasis, including S100A4/metastasin.
J. Biol. Chem.
PUBLISHED: 03-13-2009
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The integrin alpha6beta4 is associated with carcinoma progression by contributing to apoptosis resistance, invasion, and metastasis, due in part to the activation of select transcription factors. To identify genes regulated by the alpha6beta4 integrin, we compared gene expression profiles of MDA-MB-435 cells that stably express integrin alpha6beta4 (MDA/beta4) and vector-only-transfected cells (MDA/mock) using Affymetrix GeneChip analysis. Our results show that integrin alpha6beta4 altered the expression of 538 genes (p < 0.01). Of these genes, 36 are associated with pathways implicated in cell motility and metastasis, including S100A4/metastasin. S100A4 expression correlated well with integrin alpha6beta4 expression in established cell lines. Suppression of S100A4 by small interference RNA resulted in a reduced capacity of alpha6beta4-expressing cells to invade a reconstituted basement membrane in response to lysophosphatidic acid. Using small interference RNA, promoter analysis, and chromatin immunoprecipitation, we demonstrate that S100A4 is regulated by NFAT5, thus identifying the first target of NFAT5 in cancer. In addition, several genes that are known to be regulated by DNA methylation were up-regulated dramatically by integrin alpha6beta4 expression, including S100A4, FST, PDLIM4, CAPG, and Nkx2.2. Notably, inhibition of DNA methyltransferases stimulated expression of these genes in cells lacking the alpha6beta4 integrin, whereas demethylase inhibitors suppressed expression in alpha6beta4 integrin-expressing cells. Alterations in DNA methylation were confirmed by bisulfate sequencing, thus suggesting that integrin alpha6beta4 signaling can lead to the demethylation of select promoters. In summary, our data suggest that integrin alpha6beta4 confers a motile and invasive phenotype to breast carcinoma cells by regulating proinvasive and prometastatic gene expression.
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Analysis of the differential host cell nuclear proteome induced by attenuated and virulent hemorrhagic arenavirus infection.
J. Virol.
PUBLISHED: 01-27-2009
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Arenaviruses are important emerging pathogens and include a number of hemorrhagic fever viruses classified as NIAID category A priority pathogens and CDC potential biothreat agents. Infection of guinea pigs with the New World arenavirus Pichindé virus (PICV) has been used as a biosafety level 2 model for the Lassa virus. Despite continuing research, little is known about the molecular basis of pathogenesis, and this has hindered the design of novel antiviral therapeutics. Modulation of the host response is a potential strategy for the treatment of infectious diseases. We have previously investigated the global host response to attenuated and lethal arenavirus infections by using high-throughput immunoblotting and kinomics approaches. In this report, we describe the differential nuclear proteomes of a murine cell line induced by mock infection and infection with attenuated and lethal variants of PICV, investigated by using two-dimensional gel electrophoresis. Spot identification using tandem mass spectrometry revealed the involvement of a number of proteins that regulate inflammation via potential modulation of NF-kappaB activity and of several heterogeneous nuclear ribonuclear proteins. Pathway analysis revealed a potential role for transcription factor XBP-1, a transcription factor involved in major histocompatibility complex II (MHC-II) expression; differential DNA-binding activity was revealed by electrophoretic mobility shift assay, and differences in surface MHC-II expression were seen following PICV infection. These data are consistent with the results of several previous studies and highlight potential differences between transcriptional and translational regulation. This study provides a number of differentially expressed targets for further research and suggests that key events in pathogenesis may be established early in infection.
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Global transcription profiling and virulence potential of Streptococcus pneumoniae after serial passage.
Gene
PUBLISHED: 01-22-2009
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Streptococcus pneumoniae, a facultative human pathogen associated with wide variety of diseases, such as pneumonia, meningitis, sepsis and otitis media. Factors involved in the initial colonization, survival and etiology of this commensal bacteria in the human host from the ex vivo environment is still not clearly understood. Here, we report alterations in global transcriptional profiles of S. pneumoniae 6304 serotype 4 after 50 passages (50P) and 100 passages (100P) on laboratory media to better understand gene expression strategies employed by the bacterium during progression from the nasopharynx to the blood. The results show that six-fold more genes were differentially expressed after 100P as compared to 50P. After 100P on blood agar plates, 726 genes (33%) of 2192 genes in the S. pneumoniae genome were differentially expressed. Moreover, the majority of these genes (68%) were expressed at higher levels with increasing passage number and from different functional groups. Significantly, all the genes present in Region of Diversity 10 (RD10) are required for virulence during blood stream infection showed enhanced expression after passage. However, there was no significant decrease in the LD(50) of serial passage strains compare to single passage strain in a mouse challenge model. Overall, our data suggest that bacteria adapt to extended laboratory passage by substantially altering gene expression. Furthermore, extended passage on blood agar plates reduces the expression of genes associated with initial colonization and adherence but enhances the expression of genes needed for systemic infection.
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Cognitive enhancement with rosiglitazone links the hippocampal PPAR? and ERK MAPK signaling pathways.
J. Neurosci.
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We previously reported that the peroxisome proliferator-activated receptor ? (PPAR?) agonist rosiglitazone (RSG) improved hippocampus-dependent cognition in the Alzheimers disease (AD) mouse model, Tg2576. RSG had no effect on wild-type littermate cognitive performance. Since extracellular signal-regulated protein kinase mitogen-activated protein kinase (ERK MAPK) is required for many forms of learning and memory that are affected in AD, and since both PPAR? and ERK MAPK are key mediators of insulin signaling, the current study tested the hypothesis that RSG-mediated cognitive improvement induces a hippocampal PPAR? pattern of gene and protein expression that converges with the ERK MAPK signaling axis in Tg2576 AD mice. In the hippocampal PPAR? transcriptome, we found significant overlap between peroxisome proliferator response element-containing PPAR? target genes and ERK-regulated, cAMP response element-containing target genes. Within the Tg2576 dentate gyrus proteome, RSG induced proteins with structural, energy, biosynthesis and plasticity functions. Several of these proteins are known to be important for cognitive function and are also regulated by ERK MAPK. In addition, we found the RSG-mediated augmentation of PPAR? and ERK2 activity during Tg2576 cognitive enhancement was reversed when hippocampal PPAR? was pharmacologically antagonized, revealing a coordinate relationship between PPAR? transcriptional competency and phosphorylated ERK that is reciprocally affected in response to chronic activation, compared with acute inhibition, of PPAR?. We conclude that the hippocampal transcriptome and proteome induced by cognitive enhancement with RSG harnesses a dysregulated ERK MAPK signal transduction pathway to overcome AD-like cognitive deficits in Tg2576 mice. Thus, PPAR? represents a signaling system that is not crucial for normal cognition yet can intercede to restore neural networks compromised by AD.
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Innate immune tolerance and the role of kupffer cells in differential responses to interferon therapy among patients with HCV genotype 1 infection.
Gastroenterology
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In patients with hepatitis C virus (HCV) infection, interferon alfa (IFN-?) alters expression of IFN-stimulated genes (ISGs), but little is understood about factors that determine outcomes of therapy. We used a systems biology approach to evaluate the acute response of patients with chronic hepatitis C to IFN-? therapy.
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The National NeuroAIDS Tissue Consortium brain gene array: two types of HIV-associated neurocognitive impairment.
PLoS ONE
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The National NeuroAIDS Tissue Consortium (NNTC) performed a brain gene expression array to elucidate pathophysiologies of Human Immunodeficiency Virus type 1 (HIV-1)-associated neurocognitive disorders.
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Detection of structural and metabolic changes in traumatically injured hippocampus by quantitative differential proteomics.
J. Neurotrauma
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Traumatic brain injury (TBI) is a complex and common problem resulting in the loss of cognitive function. In order to build a comprehensive knowledge base of the proteins that underlie these cognitive deficits, we employed unbiased quantitative mass spectrometry, proteomics, and bioinformatics to identify and quantify dysregulated proteins in the CA3 subregion of the hippocampus in the fluid percussion model of TBI in rats. Using stable isotope 18O-water differential labeling and multidimensional tandem liquid chromatography (LC)-MS/MS with high stringency statistical analyses and filtering, we identified and quantified 1002 common proteins, with 124 increased and 76 decreased. The ingenuity pathway analysis (IPA) bioinformatics tool identified that TBI had profound effects on downregulating global energy metabolism, including glycolysis, the Krebs cycle, and oxidative phosphorylation, as well as cellular structure and function. Widespread upregulation of actin-related cytoskeletal dynamics was also found. IPA indicated a common integrative signaling node, calcineurin B1 (CANB1, CaNB?, or PPP3R1), which was downregulated by TBI. Western blotting confirmed that the calcineurin regulatory subunit, CANB1, and its catalytic binding partner PP2BA, were decreased without changes in other calcineurin subunits. CANB1 plays a critical role in downregulated networks of calcium signaling and homeostasis through calmodulin and calmodulin-dependent kinase II to highly interconnected structural networks dominated by tubulins. This large-scale knowledge base lays the foundation for the identification of novel therapeutic targets for cognitive rescue in TBI.
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Proteomics improves the prediction of burns mortality: results from regression spline modeling.
Clin Transl Sci
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Prediction of mortality in severely burned patients remains unreliable. Although clinical covariates and plasma protein abundance have been used with varying degrees of success, the triad of burn size, inhalation injury, and age remains the most reliable predictor. We investigated the effect of combining proteomics variables with these three clinical covariates on prediction of mortality in burned children. Serum samples were collected from 330 burned children (burns covering >25% of the total body surface area) between admission and the time of the first operation for clinical chemistry analyses and proteomic assays of cytokines. Principal component analysis revealed that serum protein abundance and the clinical covariates each provided independent information regarding patient survival. To determine whether combining proteomics with clinical variables improves prediction of patient mortality, we used multivariate adaptive regression splines, because the relationships between analytes and mortality were not linear. Combining these factors increased overall outcome prediction accuracy from 52% to 81% and area under the receiver operating characteristic curve from 0.82 to 0.95. Thus, the predictive accuracy of burns mortality is substantially improved by combining protein abundance information with clinical covariates in a multivariate adaptive regression splines classifier, a model currently being validated in a prospective study.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.